libSBML Python API  5.10.0
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addCVTerms.py

Adds controlled vocabulary terms to a species in a model.

1 #!/usr/bin/env python
2 ##
3 ## \file addCVTerms.py
4 ## \brief adds controlled vocabulary terms to a species in a model
5 ## \author Sarah Keating
6 ##
7 ## <!--------------------------------------------------------------------------
8 ## This sample program is distributed under a different license than the rest
9 ## of libSBML. This program uses the open-source MIT license, as follows:
10 ##
11 ## Copyright (c) 2013-2014 by the California Institute of Technology
12 ## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
13 ## and the University of Heidelberg (Germany), with support from the National
14 ## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
15 ##
16 ## Permission is hereby granted, free of charge, to any person obtaining a
17 ## copy of this software and associated documentation files (the "Software"),
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21 ## Software is furnished to do so, subject to the following conditions:
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39 ## ------------------------------------------------------------------------ -->
40 
41 import sys
42 import os.path
43 from libsbml import *
44 
45 def main (args):
46  """usage: addCVTerms <input-filename> <output-filename>
47  Adds controlled vocabulary term to a species
48  """
49  if len(args) != 3:
50  print(main.__doc__)
51  sys.exit(2)
52 
53  d = readSBML(args[1]);
54  errors = d.getNumErrors();
55 
56  if (errors > 0):
57  print("Read Error(s):");
58  d.printErrors();
59  print("Correct the above and re-run.");
60  else:
61  n = d.getModel().getNumSpecies();
62 
63  if (n <= 0):
64  print("Model has no species.\n Cannot add CV terms\n");
65  else:
66  s = d.getModel().getSpecies(0);
67 
68  cv = CVTerm();
69  cv.setQualifierType(BIOLOGICAL_QUALIFIER);
70  cv.setBiologicalQualifierType(BQB_IS_VERSION_OF);
71  cv.addResource("http://www.geneontology.org/#GO:0005892");
72 
73  cv2 = CVTerm();
74  cv2.setQualifierType(BIOLOGICAL_QUALIFIER);
75  cv2.setBiologicalQualifierType(BQB_IS);
76  cv2.addResource("http://www.geneontology.org/#GO:0005895");
77 
78  cv1 = CVTerm();
79  cv1.setQualifierType(BIOLOGICAL_QUALIFIER);
80  cv1.setBiologicalQualifierType(BQB_IS_VERSION_OF);
81  cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
82 
83  s.addCVTerm(cv);
84  s.addCVTerm(cv2);
85  s.addCVTerm(cv1);
86 
87  writeSBML(d, args[2]);
88 
89  return errors;
90 
91 
92 if __name__ == '__main__':
93  main(sys.argv)